H-2 class II histocompatibility antigen, A-B alpha chain (H2-Aa) is a 256-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P14434.
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The mean pLDDT of this model is 88.5 (confident overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 72% |
| 70 to 90 | Confident: backbone generally right | 16% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 4% |
What pLDDT means and how to read it
Membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8VQ8 | X-ray | 2.01 Å | C=26-205 |
| 8RAL | X-ray | 2.1 Å | A=24-218 |
| 1MUJ | X-ray | 2.15 Å | A=24-205 |
| 4P23 | X-ray | 2.25 Å | C=27-205 |
| 1LNU | X-ray | 2.5 Å | A/C/E/G=27-208 |
| 3C5Z | X-ray | 2.55 Å | C/G=27-208 |
| 6MNG | X-ray | 2.66 Å | C=27-205 |
| 3RDT | X-ray | 2.7 Å | C=27-208 |
| 6MNN | X-ray | 2.83 Å | C=27-205 |
| 4P46 | X-ray | 2.85 Å | C=27-205 |
| 6MNO | X-ray | 2.9 Å | C=27-205 |
| 9AUD | X-ray | 2.9 Å | C=26-205 |
| 3C60 | X-ray | 3.05 Å | C/G=27-208 |
| 6MNM | X-ray | 3.1 Å | C=27-205 |
| 6MKD | X-ray | 3.2 Å | C=27-205 |
| 4P5T | X-ray | 3.26 Å | C/G=27-208 |
| 6MKR | X-ray | 3.35 Å | C=27-205 |
| 3C6L | X-ray | 3.4 Å | C/G=27-208 |
| 9CYM | X-ray | 3.84 Å | A=24-218 |
| 9CYL | X-ray | 4.66 Å | A=24-218 |
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